PHP Basics

PHP is a widely-used general-purpose scripting language that is especially suited for Web development and can be embedded into HTML.

source: php.net

This means PHP can be used to generate HTML. This allows us to adhere to the DRY (Don’t Repeat Yourself) principle.

What makes a PHP-script

A PHP-script is identified by its .php extension and the PHP-tags in the file.

PHP tags

PHP interprets only the code enclosed within the special PHP-tags.

• Opening tag: <?php
• Closing tag: ?>

echo "Before php-tags";

<?php

echo "Within php-tags\n";

?>

echo "After php-tags";

echo "Before php-tags";

Within php-tags

echo "After php-tags";

Notice that the code outside of the PHP-tags is not interpreted and is printed out unchanged.

A valid PHP instruction generally has the form:

{{ instruction }};

Each statement must be terminated by a semicolon (;)!

An exception to this rule are loops and conditionals. These can encapsulate a block of code in curly brackets {} and thus end in a }…

Comments

Single line comments

PHP will ignore everything behind a # or //.

echo 'hello world';

// ignore this

# and ignore this

echo 'by world';

Multi-line comments

PHP will ignore everything enclosed by /* and */.

echo 'hello world';

/* ignore this

and ignore this */

echo 'by world';

Execute a PHP-script

To get acquainted with php we will start of on the command line and work our way up to PHP as a web server.

PHP at its core is a program which reads a source file, interprets the directives and prints out the result.

Basic invocation:

php <script-to-execute>.php

The above command will print the output to the STDOUT.

Hello World

The obligatory hello world.

Create a file: hello-world.php with content:

<?php

echo "Hello World";

?>

Hello World

Run it via:

php hello-world.php

on the command line.

Types and variables

Variables are a way to store some information and give the storage space a name. Via this name, the content that was stored can be retrieved.

$name = 'value to store';

PHP knows two main types of variables:

• scalars
• arrays

Scalars

A scalar variable can hold an atomic quantity. For example: one string, or one number, …

Types

PHP knows four scalar types:

Declare

Assign a value to a variable:

Generic syntax:

$varname = 'value to store';

Examples:

$int    = 123;
$float  = 4.56;
$string = 'Hello World';
$true   = true;
$false  = false;

Printing/Displaying scalars

A scalar can be printed via two methods:

• echo
• print

Echo

Generic syntax:

echo <scalar>;
echo <scalar1>, <scalar2>, ...;

Echo outputs the provided scalars.

Multiple scalars can be printed at once, just separate them by a comma ,.

Example:

echo 123;
echo 4.56;
echo 'Hello World';
echo true;
echo false;

Print

Generic syntax:

print( <scalar> );

Print can only output one scalar at the time. (This can be circumvented via concatenation…)

Example:

print( 123 );
print( 4.56 );
print( 'Hello World' );
print( true );
print( false );

String concatenation and interpolation Or single vs. double quotes

Scalars can be combined, concatenated into larger strings.

The concatenation symbol is a dot: ..

<?php

print( 'This is a string' . ' || '  . 'this is a number: '  . 42 );

This is a string || this is a number: 42

You may have already noticed that printing variables enclosed by single quotes ' doesn’t work. The literal variable name is printed instead.

<?php

$variable = 'Hello World';

echo 'The variable contains: $variable!';

The variable contains: $variable!

To instruct PHP to interpret the variables, and other special sequences, the string must be enclosed by double quotes: ".

<?php

$variable = 'Hello World';

echo "The variable contains: $variable!";

The variable contains: Hello World!

Special character sequences

The following special character sequences are interpreted by PHP and formatted accordingly…

Example:

<?php

$variable = "hello world";

echo "1. The value of the variable is: $variable.";
echo "2. The value of the variable is: $variable.\n";
echo "\t3. The value of the variable is: $variable.\n";
echo "4. The value of the variable is: \$variable.\n";
echo "5. The value of the variable is: \"$variable\".\n";

1. The value of the variable is: hello world.2. The value of the variable is: hello world.
    3. The value of the variable is: hello world.
4. The value of the variable is: $variable.
5. The value of the variable is: "hello world".

Basic arithmetic

Floats an Integers can be used in arithmetic.

Example:

<?php

$a = 42;
$b = 3.1415;
$c = 5;

echo $a + $b  . "\n";
echo $a - $b  . "\n";
echo $a * $b  . "\n";
echo $a / $b  . "\n";
echo $a % $c  . "\n";
echo $a ** $c . "\n";

45.1415
38.8585
131.943
13.369409517746
2
130691232

Arrays

Arrays are able to hold more than one item.

An item is stored in the array at a named location. If no name/key/index is explicitly specified, an numeric index from 0 to n (where n is the number of items in the array minus one) is used as the keys.

Declare

An array can be declared in two ways:

$array = array( /* list of array items */ );

$array = [ /* list of array items */ ];

The []-method can only be used from PHP version 5.4 and higher.

A normal typical array is a list of values. The keys of those values are automatically assigned, starting with zero 0 and auto incrementing for each element added.

See below for how to print and add values to arrays

<?php

$array = [1,2,3];

print_r($array);

$array[] = 'hello';

print_r($array);

Array
(
    [0] => 1
    [1] => 2
    [2] => 3
)
Array
(
    [0] => 1
    [1] => 2
    [2] => 3
    [3] => hello
)

The keys can however be specified manually:

<?php

$array = [
   'key1' => 'value1',
   'two'  => 2,
   3      => 'hello world',
];

print_r($array);

Array
(
    [key1] => value1
    [two] => 2
    [3] => hello world
)

Print/Display arrays

The function print_r can be used to print an array.

Generic syntax:

print_r( $array );

<?php

$array = array(
   'one' => 1,
   'two' => 'three',
   4     => 'four',
   'hello' => 'world'
);

print_r( $array );

Array
(
    [one] => 1
    [two] => three
    [4] => four
    [hello] => world
)

Get a value from an array

A value can be retrieved by specifying the array variable name followed by the index you wish to retrieve enclosed in square brackets:

$array[<key>];

If the key is a string, the appropriate quoting must be used.

$array['<key>'];

Example:

<?php

$array = [1,2,3];

echo $array[0] . "\n";
echo $array[1] . "\n";
echo $array[2] . "\n";

$array_assoc = [
   'key1' => "value1",
   'key2' => "value2",
   'key3' => "value3",
];

echo $array_assoc['key1'] . "\n";
echo $array_assoc['key2'] . "\n";
echo $array_assoc['key3'] . "\n";

1
2
3
value1
value2
value3

Update a value in an array

An array value can be targeted by its key. This key can also be used to update the value:

$array[<key>] = <new value>;

Example:

<?php

$array = [
   "value1",
   "value2",
   "value3",
   100 => "hundred",
   'key' => "value",
];

print_r($array);

$array['key'] = "new value for key";

$array[1] = 'index 1 now points here';

print_r($array);

Array
(
    [0] => value1
    [1] => value2
    [2] => value3
    [100] => hundred
    [key] => value
)
Array
(
    [0] => value1
    [1] => index 1 now points here
    [2] => value3
    [100] => hundred
    [key] => new value for key
)

Manipulating arrays

Add an item to the end of an array:

Adding an element at the end of an array can be accomplished by the function array_push or by the square brackets notation ($array[] = $value;).

<?php

$array = [1,2,3];

print_r( $array );

array_push( $array, 4);

print_r( $array );

// or

$array[] = 5;

print_r( $array );

Array
(
    [0] => 1
    [1] => 2
    [2] => 3
)
Array
(
    [0] => 1
    [1] => 2
    [2] => 3
    [3] => 4
)
Array
(
    [0] => 1
    [1] => 2
    [2] => 3
    [3] => 4
    [4] => 5
)

Add an item in front of an array:

Adding an element in front of an array can be accomplished by the function array_unshift.

<?php

$array = [1,2,3];

print_r( $array );

array_unshift( $array, 4 );

print_r( $array );

Array
(
    [0] => 1
    [1] => 2
    [2] => 3
)
Array
(
    [0] => 4
    [1] => 1
    [2] => 2
    [3] => 3
)

Extract the first element from an array

Extracting the first element from an array can be accomplished by the function array_shift.

<?php

$array = [1,2,3];

print_r( $array );

echo array_shift( $array ) . "\n";

print_r( $array );

Array
(
    [0] => 1
    [1] => 2
    [2] => 3
)
1
Array
(
    [0] => 2
    [1] => 3
)

Extract the last element from an array

Extracting the last element from an array can be accomplished by the function array_pop.

<?php

$array = [1,2,3];

print_r( $array );

echo array_pop( $array ) . "\n";

print_r( $array );

Array
(
    [0] => 1
    [1] => 2
    [2] => 3
)
3
Array
(
    [0] => 1
    [1] => 2
)

Count the elements in an array

Counting the elements in an array can be accomplished by the function count.

<?php

$array = [ 1, 2, 3 ];

echo count($array) . "\n";

$array[] = "Add item";

echo count($array) . "\n";

array_shift( $array );
array_shift( $array );

echo count($array) . "\n";

3
4
2

Special arrays

PHP has some special, reserved, arrays. These arrays are created and filled by PHP.

$argv

This array holds all the arguments passed to a PHP-script from the command line.

php print_r-argv.php 'arg1' 'arg2' 123 --options

Array
(
    [0] => print_r-argv.php
    [1] => arg1
    [2] => arg2
    [3] => 123
    [4] => --options
)

$_GET

The $_GET-array holds data sent to a webpage via a HTTP-get method.

This corresponds with URL parameters.

http://example.com/page.php?arg1=hello&arg2=world&end=!

Array
(
    [arg1] => hello
    [arg2] => world
    [end] => !
)

$_POST

The $_POST-array holds data sent to a webpage via a HTTP-post method.

This is typically done via a from submission…

$_SESSION

You can store inter-page data in the $_SESSION reserved array.

This inter-page data is typically:

• user info
• preferences

$_FILES

When files are uploaded, PHP stores information about these files in this array.

Example:

Array
(
    [file] => Array
        (
            [name] => MyFile.jpg
            [type] => image/jpeg
            [tmp_name] => /tmp/php/php6hst32
            [error] => UPLOAD_ERR_OK
            [size] => 98174
        )
)

Conditionals

It can be very handy to execute a piece of code only when certain requirements are met. This kind of behaviour can be accomplished via conditionals

The if language structure defines the conditions to fulfil and the accompanying block of code to run if the conditions evaluate to true (enclosed in curly brackets {}).

if( /* <condition> */ ) {

    /* execute this code here */
}

Additionally an else-block can be defined. The code in this block will be executed when the if-condition evaluated to false.

if( /* condition */ ) {

    /* execute when condition is true */
}
else {

    /* execute when condition is false */
}

On top of this, multiple conditions can be chained into an if-elseif-else construct.

if( /* condition 1 */ ) {

    /* execute when condition 1 is true */
}
elseif( /* condition 2 */ ) {

    /* execute when condition 2 is true */
}
elseif( /* condition 3 */ ) {

    /* execute when condition 3 is true */
}
else {

    /* execute when conditions 1, 2 and 3 are false */
}

Conditionals can also be nested:

if( /* condition 1 */ ) {

    if( /* condition 2 */ ) {

        /* execute when condition 1 and 2 evaluate to true */
    }
    else {

        /* execute when conditions 1 evalutes to true and condition 2 to false */
    }
}
else {

    /* execute when condition 1 evaluates to false*/
}

Comparison operators

PHP is a dynamically type language. This means the type of a variable is not set in stone but PHP will try its best to guess the types of variables and convert them (juggle them from one type to the other) where its deemed necessary.

For example:

<?php

$string = '1 as a string';

var_dump($string);

# $string to int = 1 the `+` triggers the type juggling
var_dump( $string + 0);

# -----------------------------------------------------------------------------

var_dump( '1' == 1, 1 == true, 'abc' == true );
var_dump( '1' === 1, 1 === true, 'abc' === true );

string(13) "1 as a string"
int(1)
bool(true)
bool(true)
bool(true)
bool(false)
bool(false)
bool(false)

Logical operators

Multiple comparisons can be bundled together into one condition. They are combined via the logical operators:

Example:

<?php

if( true or false ) {

   echo "`true or false` evaluated to TRUE\n";
}
else {

   echo "`true or false` evaluated to FALSE\n";
}

echo "----------------------------------------------------------------------\n";

if( !true ) {

   echo "`!true` evaluated to TRUE\n";
}
else {

   echo "`!true` evaluated to FALSE\n";
}

echo "----------------------------------------------------------------------\n";

if( true and false ) {

   echo "`true and false` evaluated to TRUE\n";
}
else {

   echo "`true and false` evaluated to FALSE\n";
}

?>

`true or false` evaluated to TRUE
----------------------------------------------------------------------
`!true` evaluated to FALSE
----------------------------------------------------------------------
`true and false` evaluated to FALSE

These logical operators can be combined at will. Brackets () can be used to enforce precedence.

<?php

if( ( 1 and 0 ) and true ) {
   echo "`( 1 and 0 ) and true` --> true\n";
}
else {
   echo "`( 1 and 0 ) and true` --> false\n";
}

if( 1 and ( 0 and true ) ) {
   echo "`1 and ( 0 and true )` --> true\n";
}
else {
   echo "`1 and ( 0 and true )` --> false\n";
}

`( 1 and 0 ) and true` --> false
`1 and ( 0 and true )` --> false

Loops

Loops enable you to repeat a block of code until a condition is met.

While

This construct will repeat until the defined condition evaluates to false:

while( /* <condition> */ ) {

    /* execute this block */
}

# This will run until interrupted by the user.

while(1) {

    echo "Use `Ctrl`+`c` to abort this loop\n";
}

<?php

$iterations = 10;

while( $iterations > 0 ) {

   echo "Countdown finished in $iterations iterations\n";
   $iterations = $iterations - 1;
}

Countdown finished in 10 iterations
Countdown finished in 9 iterations
Countdown finished in 8 iterations
Countdown finished in 7 iterations
Countdown finished in 6 iterations
Countdown finished in 5 iterations
Countdown finished in 4 iterations
Countdown finished in 3 iterations
Countdown finished in 2 iterations
Countdown finished in 1 iterations

$var = 1;

# Add or substract by 1:
$var++; // increment by 1
$var--  // decrement by 1

# Add or substract by n:
# $var += n;
# $var -= n;

$var += 3;
$var += 100;
$var -= 42;
$var -= 4;

For

For is similar to while in functionality. It also loops until a certain condition evaluates to false. The main difference is the boilerplate required to construct the loop.

The for-construct forces you to define the counter variable and the increments right in the construct.

for( <init counter>; <condition>; <increment counter> ) {

    /* execute this block */
}

Notice the semi-colons ; between each of the for-parts!

<?php

for( $counter = 0; $counter < 10; $counter++ ) {

   echo "Loop interation: $counter\n";
}

Loop interation: 0
Loop interation: 1
Loop interation: 2
Loop interation: 3
Loop interation: 4
Loop interation: 5
Loop interation: 6
Loop interation: 7
Loop interation: 8
Loop interation: 9

The for construct can also be used to loop over all elements in an array:

<?php

$array = [
   1,
   2,
   'three',
   'value'
];

print_r($array);

for( $i = 0; $i < count($array); $i++ ){

   echo "\$array has value: '". $array[$i] . "' at index $i\n";
}

Array
(
    [0] => 1
    [1] => 2
    [2] => three
    [3] => value
)
$array has value: '1' at index 0
$array has value: '2' at index 1
$array has value: 'three' at index 2
$array has value: 'value' at index 3

Foreach

The for and the while construct have their limitations regarding arrays. What if we have an array with custom keys (not a sequential list of integers…)?

We can solve this problem with the foreach construct. This construct is specifically designed to iterate over array items.

foreach( <array> as [<key-placeholder> =>] <value-placeholder>) {

    /* use key and value here*/
}

<?php

$array = [ 1, 2, 'three', 'value' ];

print_r($array);

foreach( $array as $value ) {

   echo "The obtained value is: `$value`\n";
}

# ---------------------------------------------------------------------------- #

$array = [
   1 , 2, 3,
   'key1' => 'value1',
   100 => 'hello'
];

print_r($array);

foreach( $array as $key => $value ) {

   echo "Key: `$key` has value: `$value`\n";
}

Array
(
    [0] => 1
    [1] => 2
    [2] => three
    [3] => value
)
The obtained value is: `1`
The obtained value is: `2`
The obtained value is: `three`
The obtained value is: `value`
Array
(
    [0] => 1
    [1] => 2
    [2] => 3
    [key1] => value1
    [100] => hello
)
Key: `0` has value: `1`
Key: `1` has value: `2`
Key: `2` has value: `3`
Key: `key1` has value: `value1`
Key: `100` has value: `hello`

Flow control

Sometimes (based on a condition) you want to skip a loop iteration or stop the loop prematurely. Tis can be accomplished by use of continue or break,

continue

Stop running the code in the current loop iteration and start the next iteration.

<?php

echo "Loop start\n";

for( $count = 0 ; $count < 10 ; $count++ ) {


   if( $count == 3 or $count == 6 ) {

      echo "Count is 3 or 6; start next iteration...\n";
      continue;
   }

   echo "Current count == $count\n";
}

echo "Loop end\n";

Loop start
Current count == 0
Current count == 1
Current count == 2
Count is 3 or 6; start next iteration...
Current count == 4
Current count == 5
Count is 3 or 6; start next iteration...
Current count == 7
Current count == 8
Current count == 9
Loop end

break

Stop executing the loop iteration and break out of the loop.

<?php

echo "Loop start.\n";

for( $count = 0 ; $count < 10 ; $count++ ) {


   if( $count == 3 ) {

      echo "Count is 3: stop this loop...\n";
      break;
   }

   echo "Current count == $count\n";
}

echo "Loop end.\n";

Loop start.
Current count == 0
Current count == 1
Current count == 2
Count is 3: stop this loop...
Loop end.

Commonly used (builtin) functions

isset

The isset function checks whether a PHP variable was created / assigned.

This function returns false if the tested variable isn’t declared before or is equal to null

<?php

echo "test undeclared variable\n";
var_dump( isset($some_variable) );
echo "\n";

echo "test declared variable\n";
$some_variable = "hello world";
var_dump( isset($some_variable) );
echo "\n";

echo "test null variable\n";
$some_variable = null;
var_dump( isset($some_variable) );

test undeclared variable
bool(false)

test declared variable
bool(true)

test null variable
bool(false)

empty

The empty function checks whether a PHP variable has an empty value.

Examples of empty values: null, "", 0, …

<?php

echo "test undeclared variable\n";
var_dump( empty($some_variable) );
echo "\n";

echo "test declared variable\n";
$some_variable = "hello world";
var_dump( empty($some_variable) );
echo "\n";

echo "test empty variables\n";
$some_variable = "";
var_dump( empty($some_variable) );
$some_variable = 0;
var_dump( empty($some_variable) );
$some_variable = null;
var_dump( empty($some_variable) );

test undeclared variable
bool(true)

test declared variable
bool(false)

test empty variables
bool(true)
bool(true)
bool(true)

strlen

The strlen function returns the length (number of characters) in a string.

<?php

$string =  "The length of this string is: ";
echo $string;
echo strlen( $string );

The length of this string is: 30

str_split

The str_split function parses a string into individual characters and returns an array where each item in the array corresponds to one character in the original string.

<?php

$string = "split into chars";

$array_of_chars = str_split( $string );

print_r( $array_of_chars );

Array
(
    [0] => s
    [1] => p
    [2] => l
    [3] => i
    [4] => t
    [5] =>  
    [6] => i
    [7] => n
    [8] => t
    [9] => o
    [10] =>  
    [11] => c
    [12] => h
    [13] => a
    [14] => r
    [15] => s
)

strtolower

The strtolower returns a string with all alphabetic characters converted to lowercase.

<?php

$string =  "This is a MIXED case string";
echo $string;
$string = strtolower( $string );
echo $string;

This is a MIXED case stringthis is a mixed case string

strtoupper

The strtoupper returns a string with all alphabetic characters converted to uppercase.

<?php

$string =  "This is a MIXED case string";
echo $string;
$string = strtoupper( $string );
echo $string;

This is a MIXED case stringTHIS IS A MIXED CASE STRING

explode

The explode function parses a string into individual pieces based on a delimiter and returns an array where each item in the array corresponds to a section in the original string separated by the delimiter.

<?php

$string = "This is the first section of a semicolon separated string;This is the second section;And this the third!";

$array_of_sections = explode(";", $string);

print_r( $array_of_sections );

Array
(
    [0] => This is the first section of a semicolon separated string
    [1] => This is the second section
    [2] => And this the third!
)

This function can be used to convert the lines in a file (retrieved via file_get_contents) into an array of lines.

<?php

$string = ">Random Sequence (250 nts sampled from ATGC)
GCCAATGGTATGTCAACTCAGTCTCCCCAACTCTCGTAACTGGTAGAAGG
GTGGAGCATGAATCATGCCATCCATCTCGTATTCGAATCCGTGCGCGCGG
AGCCGAATATTTAAGTATACACACCCGCAGCACGAGCATCGTACTTTGCC
TTTCCAGCATAATTATGCATGAGGTGATAGCGAGATGATTCGGGGTAATG
CCGTTGTACCCGGCCTCGGTCTTTCCGACGACGTCCCAACGCCGACACCA";

$lines = explode("\n", $string);

print_r( $lines );

Array
(
    [0] => >Random Sequence (250 nts sampled from ATGC)
    [1] => GCCAATGGTATGTCAACTCAGTCTCCCCAACTCTCGTAACTGGTAGAAGG
    [2] => GTGGAGCATGAATCATGCCATCCATCTCGTATTCGAATCCGTGCGCGCGG
    [3] => AGCCGAATATTTAAGTATACACACCCGCAGCACGAGCATCGTACTTTGCC
    [4] => TTTCCAGCATAATTATGCATGAGGTGATAGCGAGATGATTCGGGGTAATG
    [5] => CCGTTGTACCCGGCCTCGGTCTTTCCGACGACGTCCCAACGCCGACACCA
)

implode

The implode function takes an array and glue as input. The items in the array will be glued together into a new string. Each of the sections in the new output string will be separated by the glue

<?php

$array_of_sections = [
   "section 1",
   "section 2",
   "section 3",
   "section 4",
];

echo "Create a new string delimited by semicolons: \n";
echo implode(";", $array_of_sections);

echo "\n";
echo "Create a new string delimited by newlines: \n";
echo implode("\n", $array_of_sections);

Create a new string delimited by semicolons: 
section 1;section 2;section 3;section 4
Create a new string delimited by newlines: 
section 1
section 2
section 3
section 4

preg_match

Regular expressions are a very powerful way of detecting patterns in a string.

The complete depth and power of regular expressions are out of the scope of this course but we will use them to detect header lines in multifasta sequences.

<?php

echo "We want to match a leading > symbol:\n";
//       Pattern  Find pattern in this
var_dump( preg_match("/^>/",  ">MultiFasta Sequence Header") );

var_dump( preg_match("/^>/",  "Hello World") );

We want to match a leading > symbol:
int(1)
int(0)

Exercises

php count-to-number.php 9

Count up from 0 to 9: 
0
1
2
3
4
5
6
7
8
9
Count down from 9 to 0: 
9
8
7
6
5
4
3
2
1
0
Count up from 0 to 9 in steps of 3: 
0
3
6
9

php print-asterisks.php 9

*********

php print-square-of-asterisks.php 9

*********
*********
*********
*********
*********
*********
*********
*********
*********

php print-square-of-asterisks.php 15 5

***************
***************
***************
***************
***************

php print-left-bottom-balanced-triangle.php 9

*
**
***
****
*****
******
*******
********

php print-right-bottom-balanced-triangle.php 9

        *
       **
      ***
     ****
    *****
   ******
  *******
 ********
 

php print-center-bottom-balanced-triangle.php 9

     
    **
   ****
  ******
 ********

php print-left-top-balanced-triangle.php 9

*********
********
*******
******
*****
****
***
**
*

php print-right-top-balanced-triangle.php 9

*********
 ********
  *******
   ******
    *****
     ****
      ***
       **
        *

php print-center-top-balanced-triangle.php 9

*********
 *******
  *****
   ***
    *

php count-argv.php 9 12 3 5 4 1 8 5

8 arguments where provided

php number-statistics.php 9 12 3 5 4 1 8 5

The numbers received:
number 0: 9
number 1: 12
number 2: 3
number 3: 5
number 4: 4
number 5: 1
number 6: 8
number 7: 5

Smallest number: 1
Avg: 5.875
Largest number: 12
Number of numbers: 8
Number occurences
    9   ->  1
    12  ->  1
    3   ->  1
    5   ->  2
    4   ->  1
    1   ->  1
    8   ->  1

The numbers in reverse order:
number 7: 5
number 6: 8
number 5: 1
number 4: 4
number 3: 5
number 2: 3
number 1: 12
number 0: 9

Numbers from smallest to largest:
1
3
4
5
5
8
9
12

$array = array(
    'position 1' => 'hello',
    'position 2' => 'world',
    3            => 'three',
    'four'       => 4
);

php array-keys.php 

Array
(
    [0] => position 1
    [1] => position 2
    [2] => 3
    [3] => four
)

$array = array(
    'position 1' => 'hello',
    'position 2' => 'world',
    3            => 'three',
    'four'       => 4
);

php array-reverse.php 

Array
(
    [0] => 4
    [1] => three
    [2] => world
    [3] => hello
)
Array
(
    [four] => 4
    [3] => three
    [position 2] => world
    [position 1] => hello
)

php dna-reverse-complement.php 'ATGCCGATAGGACTATGGACTATCTAGAGATCTATCAGAGAATATATCCGGGATAATCGGATATCGGCGATAC'

orig.: ATGCCGATAGGACTATGGACTATCTAGAGATCTATCAGAGAATATATCCGGGATAATCGGATATCGGCGATAC
comp.: TACGGCTATCCTGATACCTGATAGATCTCTAGATAGTCTCTTATATAGGCCCTATTAGCCTATAGCCGCTATG

php dna-reverse-complement-with-bonds.php 'ATGCCGATAGGACTATGGACTATCTAGAGATCTATCAGAGAATATATCCGGGATAATCGGATATCGGCGATAC'

orig.: ATGCCGATAGGACTATGGACTATCTAGAGATCTATCAGAGAATATATCCGGGATAATCGGATATCGGCGATAC
       |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
comp.: TACGGCTATCCTGATACCTGATAGATCTCTAGATAGTCTCTTATATAGGCCCTATTAGCCTATAGCCGCTATG

php dna-reverse-complement-robust.php 'ATgCXCgAtAgg  ACTAtgGaCtA X  TCtA g aGaTc TatCAgAgaatAtiXXATCcgggATAATcggAtATCggCGaTaC'

orig.: ATgCXCgAtAgg  ACTAtgGaCtA X  TCtA g aGaTc TatCAgAgaatAtiXXATCcgggATAATcggAtATCggCGaTaC
comp.: TACGGCTATCCTGATACCTGATAGATCTCTAGATAGTCTCTTATATAGGCCCTATTAGCCTATAGCCGCTATG

Invalid NT characters:
X: 4 occurrences
i: 1 occurrences

php dna-frequency.php 'ATGCCGATAGGACTATGGACTATCTAGAGATCTATCAGAGAATATATCCGGGATAATCGGATATCGGCGATAC'

input: ATGCCGATAGGACTATGGACTATCTAGAGATCTATCAGAGAATATATCCGGGATAATCGGATATCGGCGATAC

   STATS:
      A: 24 nts -> 32.876712328767 %
      T: 18 nts -> 24.657534246575 %
      G: 18 nts -> 24.657534246575 %
      C: 13 nts -> 17.808219178082 %

   GRAPH:
      A: =================================
      T: =========================
      G: =========================
      C: ==================

php character-frequency.php 'Hello world, this is a random 123#$ string.'

input: Hello world, this is a random 123#$ string.

STATS:
'H': 1 occurences -> 2.3255813953488 %
'e': 1 occurences -> 2.3255813953488 %
'l': 3 occurences -> 6.9767441860465 %
'o': 3 occurences -> 6.9767441860465 %
' ': 7 occurences -> 16.279069767442 %
'w': 1 occurences -> 2.3255813953488 %
'r': 3 occurences -> 6.9767441860465 %
'd': 2 occurences -> 4.6511627906977 %
',': 1 occurences -> 2.3255813953488 %
't': 2 occurences -> 4.6511627906977 %
'h': 1 occurences -> 2.3255813953488 %
'i': 3 occurences -> 6.9767441860465 %
's': 3 occurences -> 6.9767441860465 %
'a': 2 occurences -> 4.6511627906977 %
'n': 2 occurences -> 4.6511627906977 %
'm': 1 occurences -> 2.3255813953488 %
'1': 1 occurences -> 2.3255813953488 %
'2': 1 occurences -> 2.3255813953488 %
'3': 1 occurences -> 2.3255813953488 %
'#': 1 occurences -> 2.3255813953488 %
'$': 1 occurences -> 2.3255813953488 %
'g': 1 occurences -> 2.3255813953488 %
'.': 1 occurences -> 2.3255813953488 %

Order by frequentie:
'H': 1 occurences -> 2.3255813953488 %
'e': 1 occurences -> 2.3255813953488 %
'w': 1 occurences -> 2.3255813953488 %
',': 1 occurences -> 2.3255813953488 %
'h': 1 occurences -> 2.3255813953488 %
'm': 1 occurences -> 2.3255813953488 %
'1': 1 occurences -> 2.3255813953488 %
'2': 1 occurences -> 2.3255813953488 %
'3': 1 occurences -> 2.3255813953488 %
'#': 1 occurences -> 2.3255813953488 %
'$': 1 occurences -> 2.3255813953488 %
'g': 1 occurences -> 2.3255813953488 %
'.': 1 occurences -> 2.3255813953488 %
'd': 2 occurences -> 4.6511627906977 %
't': 2 occurences -> 4.6511627906977 %
'a': 2 occurences -> 4.6511627906977 %
'n': 2 occurences -> 4.6511627906977 %
'l': 3 occurences -> 6.9767441860465 %
'o': 3 occurences -> 6.9767441860465 %
'r': 3 occurences -> 6.9767441860465 %
'i': 3 occurences -> 6.9767441860465 %
's': 3 occurences -> 6.9767441860465 %
' ': 7 occurences -> 16.279069767442 %

Order by character:
' ': 7 occurences -> 16.279069767442 %
'#': 1 occurences -> 2.3255813953488 %
'$': 1 occurences -> 2.3255813953488 %
',': 1 occurences -> 2.3255813953488 %
'.': 1 occurences -> 2.3255813953488 %
'H': 1 occurences -> 2.3255813953488 %
'a': 2 occurences -> 4.6511627906977 %
'd': 2 occurences -> 4.6511627906977 %
'e': 1 occurences -> 2.3255813953488 %
'g': 1 occurences -> 2.3255813953488 %
'h': 1 occurences -> 2.3255813953488 %
'i': 3 occurences -> 6.9767441860465 %
'l': 3 occurences -> 6.9767441860465 %
'm': 1 occurences -> 2.3255813953488 %
'n': 2 occurences -> 4.6511627906977 %
'o': 3 occurences -> 6.9767441860465 %
'r': 3 occurences -> 6.9767441860465 %
's': 3 occurences -> 6.9767441860465 %
't': 2 occurences -> 4.6511627906977 %
'w': 1 occurences -> 2.3255813953488 %
'1': 1 occurences -> 2.3255813953488 %
'2': 1 occurences -> 2.3255813953488 %
'3': 1 occurences -> 2.3255813953488 %